6ZY5
Cryo-EM structure of the Human topoisomerase II alpha DNA-binding/cleavage domain in State 1
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0000228 | cellular_component | nuclear chromosome |
| A | 0000287 | molecular_function | magnesium ion binding |
| A | 0000712 | biological_process | resolution of meiotic recombination intermediates |
| A | 0000775 | cellular_component | chromosome, centromeric region |
| A | 0000793 | cellular_component | condensed chromosome |
| A | 0000819 | biological_process | sister chromatid segregation |
| A | 0001673 | cellular_component | male germ cell nucleus |
| A | 0002244 | biological_process | hematopoietic progenitor cell differentiation |
| A | 0003677 | molecular_function | DNA binding |
| A | 0003682 | molecular_function | chromatin binding |
| A | 0003723 | molecular_function | RNA binding |
| A | 0003916 | molecular_function | DNA topoisomerase activity |
| A | 0003918 | molecular_function | DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity |
| A | 0005080 | molecular_function | protein kinase C binding |
| A | 0005515 | molecular_function | protein binding |
| A | 0005524 | molecular_function | ATP binding |
| A | 0005634 | cellular_component | nucleus |
| A | 0005654 | cellular_component | nucleoplasm |
| A | 0005730 | cellular_component | nucleolus |
| A | 0005737 | cellular_component | cytoplasm |
| A | 0005814 | cellular_component | centriole |
| A | 0006259 | biological_process | DNA metabolic process |
| A | 0006265 | biological_process | DNA topological change |
| A | 0006266 | biological_process | DNA ligation |
| A | 0006974 | biological_process | DNA damage response |
| A | 0007059 | biological_process | chromosome segregation |
| A | 0007143 | biological_process | female meiotic nuclear division |
| A | 0008094 | molecular_function | ATP-dependent activity, acting on DNA |
| A | 0008301 | molecular_function | DNA binding, bending |
| A | 0009330 | cellular_component | DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex |
| A | 0030261 | biological_process | chromosome condensation |
| A | 0030263 | biological_process | apoptotic chromosome condensation |
| A | 0032991 | cellular_component | protein-containing complex |
| A | 0040016 | biological_process | embryonic cleavage |
| A | 0042752 | biological_process | regulation of circadian rhythm |
| A | 0042803 | molecular_function | protein homodimerization activity |
| A | 0043065 | biological_process | positive regulation of apoptotic process |
| A | 0043130 | molecular_function | ubiquitin binding |
| A | 0045870 | biological_process | positive regulation of single stranded viral RNA replication via double stranded DNA intermediate |
| A | 0045944 | biological_process | positive regulation of transcription by RNA polymerase II |
| A | 0046872 | molecular_function | metal ion binding |
| A | 0046982 | molecular_function | protein heterodimerization activity |
| A | 0048511 | biological_process | rhythmic process |
| A | 0060255 | biological_process | regulation of macromolecule metabolic process |
| A | 1905463 | biological_process | negative regulation of DNA duplex unwinding |
| A | 1990904 | cellular_component | ribonucleoprotein complex |
| B | 0000228 | cellular_component | nuclear chromosome |
| B | 0000287 | molecular_function | magnesium ion binding |
| B | 0000712 | biological_process | resolution of meiotic recombination intermediates |
| B | 0000775 | cellular_component | chromosome, centromeric region |
| B | 0000793 | cellular_component | condensed chromosome |
| B | 0000819 | biological_process | sister chromatid segregation |
| B | 0001673 | cellular_component | male germ cell nucleus |
| B | 0002244 | biological_process | hematopoietic progenitor cell differentiation |
| B | 0003677 | molecular_function | DNA binding |
| B | 0003682 | molecular_function | chromatin binding |
| B | 0003723 | molecular_function | RNA binding |
| B | 0003916 | molecular_function | DNA topoisomerase activity |
| B | 0003918 | molecular_function | DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity |
| B | 0005080 | molecular_function | protein kinase C binding |
| B | 0005515 | molecular_function | protein binding |
| B | 0005524 | molecular_function | ATP binding |
| B | 0005634 | cellular_component | nucleus |
| B | 0005654 | cellular_component | nucleoplasm |
| B | 0005730 | cellular_component | nucleolus |
| B | 0005737 | cellular_component | cytoplasm |
| B | 0005814 | cellular_component | centriole |
| B | 0006259 | biological_process | DNA metabolic process |
| B | 0006265 | biological_process | DNA topological change |
| B | 0006266 | biological_process | DNA ligation |
| B | 0006974 | biological_process | DNA damage response |
| B | 0007059 | biological_process | chromosome segregation |
| B | 0007143 | biological_process | female meiotic nuclear division |
| B | 0008094 | molecular_function | ATP-dependent activity, acting on DNA |
| B | 0008301 | molecular_function | DNA binding, bending |
| B | 0009330 | cellular_component | DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex |
| B | 0030261 | biological_process | chromosome condensation |
| B | 0030263 | biological_process | apoptotic chromosome condensation |
| B | 0032991 | cellular_component | protein-containing complex |
| B | 0040016 | biological_process | embryonic cleavage |
| B | 0042752 | biological_process | regulation of circadian rhythm |
| B | 0042803 | molecular_function | protein homodimerization activity |
| B | 0043065 | biological_process | positive regulation of apoptotic process |
| B | 0043130 | molecular_function | ubiquitin binding |
| B | 0045870 | biological_process | positive regulation of single stranded viral RNA replication via double stranded DNA intermediate |
| B | 0045944 | biological_process | positive regulation of transcription by RNA polymerase II |
| B | 0046872 | molecular_function | metal ion binding |
| B | 0046982 | molecular_function | protein heterodimerization activity |
| B | 0048511 | biological_process | rhythmic process |
| B | 0060255 | biological_process | regulation of macromolecule metabolic process |
| B | 1905463 | biological_process | negative regulation of DNA duplex unwinding |
| B | 1990904 | cellular_component | ribonucleoprotein complex |
Functional Information from PROSITE/UniProt
| site_id | PS00177 |
| Number of Residues | 9 |
| Details | TOPOISOMERASE_II DNA topoisomerase II signature. LTEGDSAKT |
| Chain | Residue | Details |
| B | LEU459-THR467 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 2 |
| Details | ACT_SITE: O-(5'-phospho-DNA)-tyrosine intermediate => ECO:0000255|PROSITE-ProRule:PRU01384 |
| Chain | Residue | Details |
| B | TYR805 | |
| A | TYR805 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 8 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:16100112, ECO:0000269|PubMed:25202966 |
| Chain | Residue | Details |
| B | SER148 | |
| B | GLY161 | |
| A | ASN91 | |
| A | ASN120 | |
| A | SER148 | |
| A | GLY161 | |
| B | ASN120 | |
| B | ASN91 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 2 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:16100112, ECO:0000305|PubMed:25202966 |
| Chain | Residue | Details |
| A | GLN376 | |
| B | GLN376 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 2 |
| Details | BINDING: BINDING => ECO:0000255|PROSITE-ProRule:PRU00995 |
| Chain | Residue | Details |
| A | GLU461 | |
| B | GLU461 |
| site_id | SWS_FT_FI5 |
| Number of Residues | 4 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:22841979 |
| Chain | Residue | Details |
| A | ASP541 | |
| A | ASP543 | |
| B | ASP543 | |
| B | ASP541 |
| site_id | SWS_FT_FI6 |
| Number of Residues | 2 |
| Details | SITE: Interaction with DNA => ECO:0000255|PROSITE-ProRule:PRU00995 |
| Chain | Residue | Details |
| B | LYS489 | |
| A | LYS489 |
| site_id | SWS_FT_FI7 |
| Number of Residues | 14 |
| Details | SITE: Interaction with DNA => ECO:0000269|PubMed:22841979 |
| Chain | Residue | Details |
| B | LYS662 | |
| B | LYS723 | |
| B | TYR757 | |
| B | SER763 | |
| B | TRP931 | |
| A | ASN492 | |
| A | ARG661 | |
| A | LYS662 | |
| A | LYS723 | |
| A | TYR757 | |
| A | SER763 | |
| A | TRP931 | |
| B | ASN492 | |
| B | ARG661 |
| site_id | SWS_FT_FI8 |
| Number of Residues | 2 |
| Details | SITE: Transition state stabilizer => ECO:0000250|UniProtKB:P06786 |
| Chain | Residue | Details |
| B | ARG804 | |
| A | ARG804 |
| site_id | SWS_FT_FI9 |
| Number of Residues | 2 |
| Details | SITE: Important for DNA bending; intercalates between base pairs of target DNA => ECO:0000250|UniProtKB:P06786 |
| Chain | Residue | Details |
| B | ILE856 | |
| A | ILE856 |
| site_id | SWS_FT_FI10 |
| Number of Residues | 2 |
| Details | MOD_RES: N-acetylmethionine => ECO:0000269|Ref.10, ECO:0007744|PubMed:20068231, ECO:0007744|PubMed:21406692, ECO:0007744|PubMed:22814378 |
| Chain | Residue | Details |
| B | MET1 | |
| A | MET1 |
| site_id | SWS_FT_FI11 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:17081983, ECO:0007744|PubMed:18691976, ECO:0007744|PubMed:20068231, ECO:0007744|PubMed:21406692, ECO:0007744|PubMed:23186163 |
| Chain | Residue | Details |
| B | SER4 | |
| A | SER4 |
| site_id | SWS_FT_FI12 |
| Number of Residues | 4 |
| Details | MOD_RES: Phosphothreonine => ECO:0007744|PubMed:20068231 |
| Chain | Residue | Details |
| A | THR282 | |
| A | THR1205 | |
| B | THR282 | |
| B | THR1205 |
| site_id | SWS_FT_FI13 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphoserine; by CK1 => ECO:0000269|PubMed:19043076, ECO:0000269|Ref.11, ECO:0007744|PubMed:17081983, ECO:0007744|PubMed:18669648, ECO:0007744|PubMed:20068231, ECO:0007744|PubMed:21406692, ECO:0007744|PubMed:23186163 |
| Chain | Residue | Details |
| B | SER1106 | |
| A | SER1106 |
| site_id | SWS_FT_FI14 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:16964243, ECO:0007744|PubMed:17081983, ECO:0007744|PubMed:18669648, ECO:0007744|PubMed:18691976, ECO:0007744|PubMed:20068231, ECO:0007744|PubMed:21406692, ECO:0007744|PubMed:23186163 |
| Chain | Residue | Details |
| B | SER1213 | |
| A | SER1213 |
| site_id | SWS_FT_FI15 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphothreonine => ECO:0007744|PubMed:23186163 |
| Chain | Residue | Details |
| B | THR1244 | |
| A | THR1244 |
| site_id | SWS_FT_FI16 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:17081983, ECO:0007744|PubMed:17924679, ECO:0007744|PubMed:18691976, ECO:0007744|PubMed:19690332, ECO:0007744|PubMed:20068231, ECO:0007744|PubMed:21406692, ECO:0007744|PubMed:23186163 |
| Chain | Residue | Details |
| B | SER1247 | |
| A | SER1247 |
| site_id | SWS_FT_FI17 |
| Number of Residues | 10 |
| Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:21406692 |
| Chain | Residue | Details |
| B | SER1299 | |
| B | SER1302 | |
| B | SER1476 | |
| A | SER1295 | |
| A | SER1297 | |
| A | SER1299 | |
| A | SER1302 | |
| A | SER1476 | |
| B | SER1295 | |
| B | SER1297 |
| site_id | SWS_FT_FI18 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphothreonine => ECO:0000250|UniProtKB:Q01320 |
| Chain | Residue | Details |
| B | THR1327 | |
| A | THR1327 |
| site_id | SWS_FT_FI19 |
| Number of Residues | 4 |
| Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:17081983, ECO:0007744|PubMed:18669648, ECO:0007744|PubMed:18691976, ECO:0007744|PubMed:20068231, ECO:0007744|PubMed:21406692 |
| Chain | Residue | Details |
| B | SER1337 | |
| A | SER1332 | |
| A | SER1337 | |
| B | SER1332 |
| site_id | SWS_FT_FI20 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphothreonine; by PLK3 => ECO:0000269|PubMed:18062778, ECO:0007744|PubMed:17081983, ECO:0007744|PubMed:18669648, ECO:0007744|PubMed:20068231, ECO:0007744|PubMed:21406692 |
| Chain | Residue | Details |
| B | THR1343 | |
| A | THR1343 |
| site_id | SWS_FT_FI21 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:17081983, ECO:0007744|PubMed:18669648, ECO:0007744|PubMed:20068231, ECO:0007744|PubMed:21406692 |
| Chain | Residue | Details |
| B | SER1351 | |
| A | SER1351 |
| site_id | SWS_FT_FI22 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:17081983, ECO:0007744|PubMed:20068231, ECO:0007744|PubMed:21406692 |
| Chain | Residue | Details |
| B | SER1354 | |
| A | SER1354 |
| site_id | SWS_FT_FI23 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:16964243, ECO:0007744|PubMed:17081983, ECO:0007744|PubMed:19690332, ECO:0007744|PubMed:20068231, ECO:0007744|PubMed:21406692, ECO:0007744|PubMed:23186163 |
| Chain | Residue | Details |
| B | SER1374 | |
| A | SER1374 |
| site_id | SWS_FT_FI24 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:16964243, ECO:0007744|PubMed:17081983, ECO:0007744|PubMed:18691976, ECO:0007744|PubMed:20068231, ECO:0007744|PubMed:21406692, ECO:0007744|PubMed:23186163 |
| Chain | Residue | Details |
| B | SER1377 | |
| A | SER1377 |
| site_id | SWS_FT_FI25 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:19690332 |
| Chain | Residue | Details |
| B | SER1387 | |
| A | SER1387 |
| site_id | SWS_FT_FI26 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:23186163 |
| Chain | Residue | Details |
| B | SER1391 | |
| A | SER1391 |
| site_id | SWS_FT_FI27 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:18669648 |
| Chain | Residue | Details |
| B | SER1392 | |
| A | SER1392 |
| site_id | SWS_FT_FI28 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:18669648, ECO:0007744|PubMed:19690332 |
| Chain | Residue | Details |
| B | SER1393 | |
| A | SER1393 |
| site_id | SWS_FT_FI29 |
| Number of Residues | 4 |
| Details | MOD_RES: N6-acetyllysine; alternate => ECO:0000250|UniProtKB:Q01320 |
| Chain | Residue | Details |
| A | LYS1422 | |
| A | LYS1442 | |
| B | LYS1422 | |
| B | LYS1442 |
| site_id | SWS_FT_FI30 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:18669648, ECO:0007744|PubMed:23186163 |
| Chain | Residue | Details |
| B | SER1449 | |
| A | SER1449 |
| site_id | SWS_FT_FI31 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphoserine; by CK2 => ECO:0000269|PubMed:10942766, ECO:0007744|PubMed:18669648, ECO:0007744|PubMed:21406692, ECO:0007744|PubMed:23186163 |
| Chain | Residue | Details |
| B | SER1469 | |
| A | SER1469 |
| site_id | SWS_FT_FI32 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphothreonine => ECO:0007744|PubMed:18669648, ECO:0007744|PubMed:21406692 |
| Chain | Residue | Details |
| B | THR1470 | |
| A | THR1470 |
| site_id | SWS_FT_FI33 |
| Number of Residues | 4 |
| Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:18669648, ECO:0007744|PubMed:20068231, ECO:0007744|PubMed:21406692, ECO:0007744|PubMed:23186163 |
| Chain | Residue | Details |
| A | SER1471 | |
| A | SER1474 | |
| B | SER1471 | |
| B | SER1474 |
| site_id | SWS_FT_FI34 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:20068231, ECO:0007744|PubMed:23186163 |
| Chain | Residue | Details |
| B | SER1495 | |
| A | SER1495 |
| site_id | SWS_FT_FI35 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:18220336, ECO:0007744|PubMed:19690332, ECO:0007744|PubMed:20068231, ECO:0007744|PubMed:23186163 |
| Chain | Residue | Details |
| B | SER1504 | |
| A | SER1504 |
| site_id | SWS_FT_FI36 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:16964243, ECO:0007744|PubMed:17081983, ECO:0007744|PubMed:18669648, ECO:0007744|PubMed:19690332, ECO:0007744|PubMed:20068231, ECO:0007744|PubMed:21406692 |
| Chain | Residue | Details |
| B | SER1525 | |
| A | SER1525 |
| site_id | SWS_FT_FI37 |
| Number of Residues | 66 |
| Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2) => ECO:0007744|PubMed:28112733 |
| Chain | Residue | Details |
| B | LYS157 | |
| B | LYS261 | |
| B | LYS352 | |
| B | LYS386 | |
| B | LYS397 | |
| B | LYS416 | |
| B | LYS418 | |
| B | LYS425 | |
| B | LYS440 | |
| B | LYS466 | |
| B | LYS480 | |
| B | LYS529 | |
| B | LYS584 | |
| B | LYS599 | |
| B | LYS614 | |
| B | LYS622 | |
| B | LYS625 | |
| B | LYS632 | |
| B | LYS655 | |
| B | LYS1114 | |
| B | LYS1204 | |
| B | LYS1259 | |
| B | LYS1276 | |
| B | LYS1283 | |
| B | LYS1286 | |
| B | LYS1363 | |
| B | LYS1367 | |
| B | LYS1373 | |
| B | LYS1454 | |
| B | LYS1459 | |
| B | LYS1484 | |
| A | LYS17 | |
| A | LYS156 | |
| A | LYS157 | |
| A | LYS261 | |
| A | LYS352 | |
| A | LYS386 | |
| A | LYS397 | |
| A | LYS416 | |
| A | LYS418 | |
| A | LYS425 | |
| A | LYS440 | |
| A | LYS466 | |
| A | LYS480 | |
| A | LYS529 | |
| A | LYS584 | |
| A | LYS599 | |
| A | LYS614 | |
| A | LYS622 | |
| A | LYS625 | |
| A | LYS632 | |
| A | LYS655 | |
| A | LYS1114 | |
| A | LYS1204 | |
| A | LYS1259 | |
| A | LYS1276 | |
| A | LYS1283 | |
| A | LYS1286 | |
| A | LYS1363 | |
| A | LYS1367 | |
| A | LYS1373 | |
| A | LYS1454 | |
| A | LYS1459 | |
| A | LYS1484 | |
| B | LYS17 | |
| B | LYS156 |
| site_id | SWS_FT_FI38 |
| Number of Residues | 4 |
| Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2) => ECO:0007744|PubMed:25218447, ECO:0007744|PubMed:28112733 |
| Chain | Residue | Details |
| B | LYS1492 | |
| A | LYS1492 |
| site_id | SWS_FT_FI39 |
| Number of Residues | 10 |
| Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2) => ECO:0007744|PubMed:25772364, ECO:0007744|PubMed:28112733 |
| Chain | Residue | Details |
| B | LYS639 | |
| B | LYS676 | |
| B | LYS1196 | |
| A | LYS639 | |
| A | LYS662 | |
| A | LYS676 | |
| A | LYS1075 | |
| A | LYS1196 | |
| B | LYS662 | |
| B | LYS1075 |
| site_id | SWS_FT_FI40 |
| Number of Residues | 2 |
| Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2) => ECO:0007744|PubMed:25218447, ECO:0007744|PubMed:25755297, ECO:0007744|PubMed:25772364, ECO:0007744|PubMed:28112733 |
| Chain | Residue | Details |
| B | LYS1228 | |
| A | LYS1228 |
| site_id | SWS_FT_FI41 |
| Number of Residues | 2 |
| Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2); alternate => ECO:0007744|PubMed:25114211, ECO:0007744|PubMed:25218447, ECO:0007744|PubMed:25755297, ECO:0007744|PubMed:25772364, ECO:0007744|PubMed:28112733 |
| Chain | Residue | Details |
| B | LYS1240 | |
| A | LYS1240 |
| site_id | SWS_FT_FI42 |
| Number of Residues | 2 |
| Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2) => ECO:0007744|PubMed:25218447, ECO:0007744|PubMed:25772364, ECO:0007744|PubMed:28112733 |
| Chain | Residue | Details |
| B | LYS1385 | |
| A | LYS1385 |
| site_id | SWS_FT_FI43 |
| Number of Residues | 2 |
| Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2); alternate => ECO:0007744|PubMed:28112733 |
| Chain | Residue | Details |
| B | LYS1422 | |
| A | LYS1422 |
| site_id | SWS_FT_FI44 |
| Number of Residues | 2 |
| Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2); alternate => ECO:0007744|PubMed:25772364, ECO:0007744|PubMed:28112733 |
| Chain | Residue | Details |
| B | LYS1442 | |
| A | LYS1442 |
